void CylBase::matchCubeMeshEntries( const ChemCompt* compt,
const CylBase& parent,
unsigned int startIndex,
double granularity,
vector< VoxelJunction >& ret,
bool useCylinderCurve, bool useCylinderCap ) const
{
const CubeMesh* other = dynamic_cast< const CubeMesh* >( compt );
assert( other );
const double EPSILON = 1e-18;
Vec a( parent.x_ - x_, parent.y_ - y_, parent.z_ - z_ );
Vec u;
Vec v;
a.orthogonalAxes( u, v );
double h = selectGridSize( other->getDx(), parent.dia_/2, granularity );
double lambda = length_ / numDivs_;
unsigned int num = floor( 0.1 + lambda / h );
// March along axis of cylinder.
// q is the location of the point along axis.
double rSlope = ( dia_ - parent.dia_ ) * 0.5 / length_;
for ( unsigned int i = 0; i < numDivs_; ++i ) {
vector< double >area( other->getNumEntries(), 0.0 );
if ( useCylinderCurve ) {
for ( unsigned int j = 0; j < num; ++j ) {
unsigned int m = i * num + j;
double frac = ( m * h + h/2.0 ) / length_;
double q0 = x_ + a.a0() * frac;
double q1 = y_ + a.a1() * frac;
double q2 = z_ + a.a2() * frac;
// get radius of cylinder at this point.
double r = dia_/2.0;
if ( !isCylinder_ ) // Use the more complicated conic value
r = parent.dia_/2.0 + frac * rSlope;
fillPointsOnCircle( u, v, Vec( q0, q1, q2 ),
h, r, area, other );
}
}
if ( useCylinderCap && i == numDivs_ - 1 ) {
fillPointsOnDisc( u, v, Vec( x_, y_, z_ ),
h, dia_/2.0, area, other );
}
// Go through all cubeMesh entries and compute diffusion
// cross-section. Assume this is through a membrane, so the
// only factor relevant is area. Not the distance.
for ( unsigned int k = 0; k < area.size(); ++k ) {
if ( area[k] > EPSILON ) {
ret.push_back( VoxelJunction( i + startIndex, k, area[k] ));
}
}
}
}
void CylMesh::matchCubeMeshEntries( const CubeMesh* other,
vector< VoxelJunction >& ret ) const
{
const double EPSILON = 1e-18;
Vec a( x1_ - x0_, y1_ - y0_, z1_ - z0_ );
Vec u;
Vec v;
a.orthogonalAxes( u, v );
double h = selectGridVolume( other->getDx() );
unsigned int num = floor( 0.1 + diffLength_ / h );
// March along axis of cylinder.
// q is the location of the point along axis.
for ( unsigned int i = 0; i < numEntries_; ++i ) {
vector< double >area( other->getNumEntries(), 0.0 );
for ( unsigned int j = 0; j < num; ++j ) {
unsigned int m = i * num + j;
double frac = ( m * h + h/2.0 ) / totLen_;
double q0 = x0_ + a.a0() * frac;
double q1 = y0_ + a.a1() * frac;
double q2 = z0_ + a.a2() * frac;
// get radius of cylinder at this point.
double r = r0_ + ( m * h + h / 2.0 ) * rSlope_;
fillPointsOnCircle( u, v, Vec( q0, q1, q2 ),
h, r, area, other );
}
// Go through all cubeMesh entries and compute diffusion
// cross-section. Assume this is through a membrane, so the
// only factor relevant is area. Not the distance.
for ( unsigned int k = 0; k < area.size(); ++k ) {
if ( area[k] > EPSILON ) {
ret.push_back( VoxelJunction( i, k, area[k] ) );
}
}
}
}
